@BigBenAussie
It's not that no one has thought about "your" method, the problem is the level of integration this would provide, how would you "greenscreen" out the emulated AmigaOS desktop elements (affectively layers) and "superimpose" those elements (layers) AND integrate those into the host windowing system (every layer must apperar to be a native one) without hacking/patching the emulated KS/OS ?
If you look at Georg's (the AROS dev that did something similar) "greenscreen" method then look specifically at 0:01:05 when he clicks the depth gadget, the window only goes to the rear of the UEA/AmigaOS instance windows, NOT to the rear of host windows, this gives you a fact, with this method all UAE/AmigaOS windows (layers) are only one single "alpha-blended" layer in the host OS.